#!/usr/bin/python
import wx
import numpy
import sys
from pySAXS.LS import absorptionXRL
import xraylib
from pySAXS.tools import isNumeric
'''
29/08/2012 OT : rename file and class LSAbsDlg to LSAbsorptionDlg
15/06/2009 OT : change from Dialog to Frame
Add Label for NIST
Change size of Frame
initial work by Antoine Thill
'''
[docs]class AbsorptionForm(wx.Frame):
def __init__(self, parent, set_dir = None,printout=None):
wx.Frame.__init__(self, parent, -1, "X-Ray absorption tool using Xraylib", \
size=wx.Size(580,650),\
pos=wx.DefaultPosition,style = wx.DEFAULT_DIALOG_STYLE)
if dir(parent).__contains__('favicon'):
wx.Frame.SetIcon(self,parent.favicon)
self.printout=printout
self.energy=8.03
self.SetBackgroundColour(wx.LIGHT_GREY)
self.res=numpy.array([0.,0.,0.])
self.Z=0
self.ActiveFormula=""
self.ActiveAtomes=numpy.zeros(120)
self.ChampText = wx.StaticText(self, 101, "click to select atoms", wx.Point(200, 100))
#energy slider and buttons
# the current NRJ is obtained with NRJslider.GetValue() in eV
self.NRJlabel = wx.StaticText(self, -1, "Energy (keV)", wx.Point(20, 20))
self.NRJTextCtrl=wx.TextCtrl(self,104,"",wx.Point(100,20),wx.Size(100,20))
self.NRJTextCtrl.SetValue(str(self.energy))
#self.Bind(wx.EVT_TEXT, self.NRJUpdate)
if self.energy!=0:
lambdaValue=xraylib.KEV2ANGST/self.energy
self.LambdaLabel= wx.StaticText(self, -1, "Lambda (Angstrom) = "+str(lambdaValue), wx.Point(250, 20))
'''
self.NRJslider=wx.Slider(self,104,8030,1000,50000,\
wx.Point(20,20),\
wx.Size(200,15),\
wx.SL_HORIZONTAL|wx.SL_AUTOTICKS)
self.NRJslider.SetTickFreq(5000,1)
self.Bind(wx.EVT_SLIDER, self.sliderUpdate)
self.NRJText = wx.StaticText(self, 105, "8.03 keV", wx.Point(250, 15))'''
self.CommonsourceText = wx.StaticText(self, -1, "Common x-ray source :", wx.Point(50, 52))
for i in range(len(absorptionXRL.COMMON_XRAY_SOURCE_MATERIALS)):
Beg=1
# H button
self.buttonSource =wx.Button(self, 1000+i, absorptionXRL.COMMON_XRAY_SOURCE_MATERIALS[i], wx.Point(200+i*35,47),wx.Size(30,30))
self.Bind(wx.EVT_BUTTON, self.OnClickSource, self.buttonSource)
self.ResetButton =wx.Button(self, 106, "Reset", wx.Point(520,12),wx.Size(50,30))
wx.EVT_BUTTON(self, 106, self.OnResetClick)
'''
#Check box for musrho or musrhoen
self.MuenBox=wx.CheckBox(self,107,"Mu_en ",(450,15))
self.Bind(wx.EVT_CHECKBOX, self.CheckBoxUpdate)
self.MuenBox.SetValue(1)
'''
self.button=[]
#################
#Definition des bouttons de chaque atome pris en charge dans le module
#################
Bcol=20
Blig=100
Bsiz=30
Znb=1
# H button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+17*Bsiz
# He button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=20
Blig=Blig+Bsiz
# Li button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# Be button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+11*Bsiz
# B button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# C button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# N button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# O button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# F button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# Ne button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=20
Blig=Blig+Bsiz
# Na button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# Mg button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+11*Bsiz
# Al button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# Si button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# P button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# S button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# Cl button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# Ar button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=20
Blig=Blig+Bsiz
#ligne 4
for n in numpy.arange(18):
# next button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
Bcol=20
Blig=Blig+Bsiz
#ligne 5
for n in numpy.arange(18):
# next button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
Bcol=20
Blig=Blig+Bsiz
# Cs button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# Ba button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# La button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
#Lanthanides line
Bcol=20
Blig=Blig+3*Bsiz
for n in numpy.arange(14):
# next button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
#fin de la ligne 6
Bcol=20+3*Bsiz
Blig=Blig-3*Bsiz
for n in numpy.arange(15):
# next button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
Bcol=20
Blig=Blig+Bsiz
# Fr button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# Ra button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
# Ac button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
#Acthinides line
Bcol=20
Blig=Blig+3*Bsiz
for n in numpy.arange(3):
# next button
self.button =wx.Button(self, Znb, xraylib.AtomicNumberToSymbol(Znb), wx.Point(Bcol,Blig),wx.Size(Bsiz,Bsiz))
self.Bind(wx.EVT_BUTTON, self.OnClick, self.button)
Znb=Znb+1
Bcol=Bcol+Bsiz
decal=50
self.SymboleText = wx.StaticText(self, 101, "Symbole = ", wx.Point(20, 365+decal))
self.NameText = wx.StaticText(self, 101, "Name = ", wx.Point(20, 380+decal))
self.ZText = wx.StaticText(self, 101, "Atomic number = ", wx.Point(20, 395+decal))
self.MasseText = wx.StaticText(self, 101, "Atomic weight = ", wx.Point(20, 410+decal))
self.MuText = wx.StaticText(self, 101, "Mu_en/rho = ", wx.Point(20, 425+decal))
# Add button
self.AtomsNumberLabel=wx.StaticText(self,1092,"Number of atoms = ",wx.Point(20,455+decal))
self.AtomsNumber=wx.TextCtrl(self,1091,"",wx.Point(130,453+decal),wx.Size(50,20))
self.AtomsNumber.SetValue("1.0")
#self.Bind(wx.EVT_TEXT, self.ThicknessUpdate)
self.Addbutton=wx.Button(self, 108, "Add", wx.Point(20,475+decal),wx.Size(50,30))
wx.EVT_BUTTON(self, 108, self.OnAddClick)
# Remove button
self.RemoveButton =wx.Button(self, 109, "Remove", wx.Point(70,475+decal),wx.Size(60,30))
wx.EVT_BUTTON(self, 109, self.OnRemoveClick)
# Remove all button
self.RemoveButton =wx.Button(self, 1090, "Remove All", wx.Point(130,475+decal),wx.Size(80,30))
wx.EVT_BUTTON(self, 1090, self.OnRemoveAllClick)
self.FormulaLabel=wx.StaticText(self,110,"Active Formula = ",wx.Point(250,350+decal))
self.CompoundMuLabel=wx.StaticText(self,112,"Compound Mu_en/rho = ",wx.Point(250,370+decal))
self.DensityLabel=wx.StaticText(self,113,"Density = ",wx.Point(250,390+decal))
self.DensityText=wx.TextCtrl(self,114,"",wx.Point(375,390+decal),wx.Size(75,20))
self.DensityText.SetValue("1.00")
#self.Bind(wx.EVT_TEXT, self.DensityUpdate)
self.DensityUnitLabel=wx.StaticText(self,115,"(g/cm3)",wx.Point(500,390+decal))
self.CompoundEDLabel=wx.StaticText(self,116,"Electronic density = ",wx.Point(250,410+decal))
self.CompoundSLLabel=wx.StaticText(self,117,"Scattering length density = ",wx.Point(250,430+decal))
self.ThicknessLabel=wx.StaticText(self,118,"Thickness = ",wx.Point(250,450+decal))
self.ThicknessText=wx.TextCtrl(self,119,"",wx.Point(375,450+decal),wx.Size(75,20))
self.ThicknessText.SetValue("0.1")
self.Bind(wx.EVT_TEXT, self.UpdateFormula)
self.ThicknessUnitLabel=wx.StaticText(self,120,"(cm)",wx.Point(500,450+decal))
self.TransLabel=wx.StaticText(self,121,"X-ray trans = ",wx.Point(250,470+decal))
self.QuitButton=wx.Button(self,wx.ID_EXIT,"QUIT",wx.Point(275,500+decal),wx.Size(75,30))
wx.EVT_BUTTON(self, wx.ID_EXIT, self.OnExitClick)
self.Bind(wx.EVT_CLOSE, self.OnExitClick)
#XRAY LIB
self.NISTLabel=wx.StaticText(self,129,"Datas from xraylib libraries",wx.Point(100,550+decal))
self.NISTLabel.SetForegroundColour('blue')
[docs] def OnResetClick(self,event):
self.Z=0
'''self.NRJslider.SetValue(8028)
self.NRJText.SetLabel(str(self.NRJslider.GetValue()/1000.0) +" keV")'''
self.energy=8.03
self.NRJTextCtrl.SetValue(str(self.energy))
self.ChampText.SetLabel("click to select an atom")
self.SymboleText.SetLabel("Symbole = ")
self.NameText.SetLabel("Name = " )
self.ZText.SetLabel("Atomic number = ")
self.MasseText.SetLabel("Atomic weight = ")
self.UpdateFormula()
####
#On clique sur l'un des bouttons du tableau
####
[docs] def OnClick(self,event):
#self.DensityText.SetValue(absorptionXRL.ATOMS[event.GetId()-1])
Z=event.GetId()
self.SymboleText.SetLabel("Symbol = " + xraylib.AtomicNumberToSymbol(Z))
self.NameText.SetLabel("Name = " + absorptionXRL.getNameZ(Z))
self.ZText.SetLabel("Atomic number : " + str(Z))
self.Z=Z
self.MasseText.SetLabel("Atomic weight : "+ str(xraylib.AtomicWeight(Z)))
self.MuText.SetLabel("Mu/rho = " + str(absorptionXRL.getMuZ(Z,self.energy)))
[docs] def UpdateFormula(self,verbose=False):
Tr=-1
ED=-1
SLD=-1
#print "Fupdate"
energy=self.NRJTextCtrl.GetValue()
if isNumeric.isNumeric(energy):
self.energy=float(energy)
if self.energy!=0:
lambdaValue=xraylib.KEV2ANGST/self.energy
self.LambdaLabel.SetLabel("Lambda (Angstrom) = "+str(lambdaValue))
self.ActiveFormula=""
#If at least one atome exist
if sum(self.ActiveAtomes)!=0:
N=self.ActiveAtomes.take(numpy.where(self.ActiveAtomes!=0)[0])
ind=numpy.where(self.ActiveAtomes!=0)[0]
j=0
for i in ind:
#self.ActiveFormula=self.ActiveFormula + str(absorptionXRL.ATOMS[int(i)]) + ' ' + str(int(N[int(j)])) + ' '
self.ActiveFormula=self.ActiveFormula + xraylib.AtomicNumberToSymbol(int(i)+1) + ' ' + str(N[int(j)]) + ' '
j=j+1
self.FormulaLabel.SetLabel("Active Formula = "+self.ActiveFormula.strip())
MuRho=absorptionXRL.getMuFormula(self.ActiveFormula,self.energy)
self.CompoundMuLabel.SetLabel("Compound Mu/rho = %1.5f (cm2/g)" % MuRho)
density=self.DensityText.GetValue()
if isNumeric.isNumeric(density):
density=float(density)
ED=absorptionXRL.getElectronDensity(self.ActiveFormula,density)[0]
self.CompoundEDLabel.SetLabel("Electronic density = %1.5e (1/cm3)" % ED)
SLD=absorptionXRL.getElectronDensity(self.ActiveFormula,density)[1]
self.CompoundSLLabel.SetLabel("Scattering length density = %1.5e (1/cm2)" % SLD)
if isNumeric.isNumeric(self.ThicknessText.GetValue()):
thickness=float(self.ThicknessText.GetValue())
Tr=absorptionXRL.getTransmission(self.ActiveFormula,\
thickness,\
density,\
self.energy)
#self.TransLabel.SetLabel("X-ray transmission = %1.5e" % numpy.exp(-float(self.DensityText.GetValue())*absorptionXRL.getMuFormula(self.ActiveFormula,self.NRJslider.GetValue()/1000.,self.MuenBox.GetValue())*float(self.ThicknessText.GetValue())))
self.TransLabel.SetLabel("X-ray transmission = %1.5e" % Tr)
if verbose:
self.printTXT("------ Absorption tools using xraylib -----")
self.printTXT("Energy : (keV) ", self.energy)
self.printTXT("Compound formula: ", self.ActiveFormula)
self.printTXT("Compound Mu_en/rho = (cm2/g) ",MuRho)
self.printTXT("Electronic density = (1/cm3) ",ED)
self.printTXT("Scattering length density = (1/cm2) ",SLD)
self.printTXT("X-ray transmission = ",Tr)
else:
try:
self.FormulaLabel.SetLabel("Active Formula = ")
self.CompoundMuLabel.SetLabel("Compound Mu_en/rho = (cm2/g)")
self.CompoundEDLabel.SetLabel("Electronic density = (1/cm3)")
self.CompoundSLLabel.SetLabel("Scattering length density = (1/cm2)")
self.TransLabel.SetLabel("X-ray transmission = ")
except:
pass
[docs] def OnAddClick(self,event):
an=self.AtomsNumber.GetValue()
if isNumeric.isNumeric(an):
an=float(an)
an=abs(an)
else:
an=1.0
if self.Z!= 0:
if self.ActiveAtomes[self.Z-1] != 0 :
#The new Atome is already present
self.ActiveAtomes[self.Z-1]=self.ActiveAtomes[self.Z-1]+an
else :
#its a brend new atome
self.ActiveAtomes[self.Z-1]=an
self.UpdateFormula()
[docs] def OnRemoveClick(self,event):
if self.Z != 0:
if self.ActiveAtomes[self.Z-1] != 0:
if self.ActiveAtomes[self.Z-1]<=1:
#It has to be removed
self.ActiveAtomes[self.Z-1]=0
else:
#One atome has to be removed
self.ActiveAtomes[self.Z-1]=self.ActiveAtomes[self.Z-1]-1
self.UpdateFormula()
[docs] def OnClickSource(self,event):
sourceID=1000-event.GetId()
source=absorptionXRL.COMMON_XRAY_SOURCE_MATERIALS[sourceID]
energy=absorptionXRL.getEnergyFromSource(source)
self.NRJTextCtrl.SetValue(str(energy))
[docs] def printTXT(self,txt="",par=""):
'''
for printing messages
'''
if self.printout==None:
print(str(txt)+str(par))
else:
self.printout(txt,par)
#######
if __name__== '__main__':
app = wx.PySimpleApp()
frame=AbsorptionForm(None, -1)
frame.Show()
app.MainLoop()